Download locality data

Clear workspace

rm(list = ls())

library(bigrquery)
library(stringr)
library(tidyverse)
library(dplyr)
library(lme4)
library(MuMIn)
library(scales)

response <- try(system('~/google-cloud-sdk/bin/gcloud projects list --quiet', intern = T))
projectid <- strsplit(response[2], " ")[[1]][1]

create_dataset <- function(poolname) {
  sql <- str_replace_all("SELECT 
    ##POOL_NAME##.percentage_of_regional_pool_present,
    ##POOL_NAME##.difference_from_locality_trait_gravity,
    ##POOL_NAME##.percentage_of_niches_present,
    ##POOL_NAME##.percentage_of_niches_2_present,
    ##POOL_NAME##.percentage_of_niches_3_present,
    latitude,
    longitude,
    percentage_landcover_5km.closed_forest_total AS closed_forest,
    percentage_landcover_5km.cultivated,
    percentage_landcover_5km.herbaceous_vegetation,
    percentage_landcover_5km.herbaceous_wetland,
    percentage_landcover_5km.open_forest_total AS open_forest,
    percentage_landcover_5km.permanent_water,
    percentage_landcover_5km.shrubs,
    percentage_landcover_5km.urban,
    percentage_landcover_5km.elevation.mean AS mean_elevation,
    percentage_landcover_5km.elevation.delta AS elevation_delta,
    average_population_density.within_5km AS average_population_density,
    urban_area.name AS city_name,
    urban_area.location.continent,
    urban_area.ecosystem.realm,
    urban_area.ecosystem.biome.biome_name AS biome,
    urban_area.country_economy.gdp_estimate_thousand_dollars_per_person AS national_gdp_estimate_thousand_dollars_per_person,
    urban_area.country_economy.income_group AS national_income_group,
    locality_id
FROM model.urban_hotspot
JOIN model2.all_species USING(locality_id, city_id)
JOIN model.urban_area USING (city_id)", '##POOL_NAME##', poolname)

  print(sql)
  
  tb <- bq_project_query(projectid, sql)

  bq_table_download(tb)
}

load_dataset <- function(poolname) {
  filename <- str_replace('hotspot_metrics_##POOL_NAME##.csv', '##POOL_NAME##', poolname)
  
  if (!file.exists(filename)) {
    data <- create_dataset(poolname)
    write_csv(data, filename)
  }
  
  
  data <- read_csv(filename)
  
  data$city_name = as.factor(data$city_name)
  data$continent = relevel(as.factor(data$continent), ref = "Europe")
  data$realm = relevel(as.factor(data$realm), ref = "Palearctic")
  data$biome = as.factor(data$biome)
  data$national_income_group = as.factor(data$national_income_group)
  data$mean_elevation_scaled = rescale(data$mean_elevation, to = c(0, 1), from = range(data$mean_elevation, na.rm = TRUE, finite = TRUE))
  data$elevation_delta_scaled = rescale(data$elevation_delta, to = c(0, 1), from = range(data$elevation_delta, na.rm = TRUE, finite = TRUE))
  data$average_population_density_scaled = rescale(data$average_population_density, to = c(0, 1), from = range(data$average_population_density, na.rm = TRUE, finite = TRUE))
  data$national_gdp_estimate_thousand_dollars_per_person_scaled = rescale(data$national_gdp_estimate_thousand_dollars_per_person, to = c(0, 1), from = range(data$national_gdp_estimate_thousand_dollars_per_person, na.rm = TRUE, finite = TRUE))
  data$latitude_scaled = rescale(data$latitude, to = c(0, 1), from = range(data$latitude, na.rm = TRUE, finite = TRUE))
  data$longitude_scaled = rescale(data$longitude, to = c(0, 1), from = range(data$longitude, na.rm = TRUE, finite = TRUE))
  data$absolute_latitude_scaled = abs(data$latitude_scaled)
  data
}

Merlin

merlin <- load_dataset('merlin')

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  city_name = col_character(),
  continent = col_character(),
  realm = col_character(),
  biome = col_character(),
  national_income_group = col_character(),
  locality_id = col_character()
)
ℹ Use `spec()` for the full column specifications.

merlin

Birdlife

birdlife <- load_dataset('birdlife')

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  city_name = col_character(),
  continent = col_character(),
  realm = col_character(),
  biome = col_character(),
  national_income_group = col_character(),
  locality_id = col_character()
)
ℹ Use `spec()` for the full column specifications.

birdlife

Both

both <- load_dataset('both')

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  city_name = col_character(),
  continent = col_character(),
  realm = col_character(),
  biome = col_character(),
  national_income_group = col_character(),
  locality_id = col_character()
)
ℹ Use `spec()` for the full column specifications.

both

Either

either <- load_dataset('either')

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  city_name = col_character(),
  continent = col_character(),
  realm = col_character(),
  biome = col_character(),
  national_income_group = col_character(),
  locality_id = col_character()
)
ℹ Use `spec()` for the full column specifications.

either

population_growth <- function(city_row) {
  population <- c(city_row$pop1950, city_row$pop1955, city_row$pop1960, city_row$pop1965, city_row$pop1970, city_row$pop1975, city_row$pop1980, city_row$pop1985, city_row$pop1990, city_row$pop1995, city_row$pop2000, city_row$pop2005, city_row$pop2010, city_row$pop2015, city_row$pop2020)
  years <- c(1950, 1955, 1960, 1965, 1970, 1975, 1980, 1985, 1990, 1995, 2000, 2005, 2010, 2015, 2020)
  
  model <- lm(population ~ years)
  model$coefficients[2]
}

city_data <- read_csv('city_data.csv')

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  .default = col_double(),
  name = col_character(),
  city_includes_estuary = col_logical(),
  region_100km_includes_estuary = col_logical(),
  region_50km_includes_estuary = col_logical(),
  region_20km_includes_estuary = col_logical(),
  biome_name = col_character(),
  realm = col_character()
)
ℹ Use `spec()` for the full column specifications.

city_data$realm <- as.factor(city_data$realm)
city_data$city_includes_estuary <- as.factor(city_data$city_includes_estuary)
city_data$region_100km_includes_estuary <- as.factor(city_data$region_100km_includes_estuary)
city_data$region_50km_includes_estuary <- as.factor(city_data$region_50km_includes_estuary)
city_data$region_20km_includes_estuary <- as.factor(city_data$region_20km_includes_estuary)
city_data$biome_name <- as.factor(city_data$biome_name)

city_data$population_growth = 0

for(i in 1:nrow(city_data)) {
    city_data[i,]$population_growth = population_growth(city_data[i,])
}

city_data